X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FDBRefEntryI.java;h=701acb663ce60ad3b3e5fe30fa5d437f5b40a210;hb=168ef5a045478ef56a5d9f8c71fbddb53a6b8a58;hp=731c25895417568cabe3acb9b86a8b770d960920;hpb=1503bcb2b548b7f6bc11bcbf081455ab94839099;p=jalview.git

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index 731c258..701acb6 100644
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -1,19 +1,97 @@
 package jalview.api;
 
+import jalview.datamodel.Mapping;
+
+//JBPComment: this is a datamodel API - so it should be in datamodel (it's a peer of SequenceI)
 
 public interface DBRefEntryI
 {
   public boolean equalRef(DBRefEntryI entry);
 
+  /**
+   * 
+   * @return Source DB name for this entry
+   */
   public String getSource();
 
-  public String getVersion();
-
+  /**
+   * 
+   * @return Accession Id for this entry
+   */
   public String getAccessionId();
 
+  /**
+   * 
+   * @param accessionId
+   *          Accession Id for this entry
+   */
   public void setAccessionId(String accessionId);
 
+  /**
+   * 
+   * @param source
+   *          Source DB name for this entry
+   */
   public void setSource(String source);
 
+  /**
+   * 
+   * @return Source DB version for this entry
+   */
+  public String getVersion();
+
+  /**
+   * 
+   * @param version
+   *          Source DB version for this entry
+   */
   public void setVersion(String version);
+
+  /**
+   * access a mapping, if present that can be used to map positions from the
+   * associated dataset sequence to the DBRef's sequence frame.
+   * 
+   * @return null or a valid mapping.
+   */
+  public Mapping getMap();
+
+  /**
+   * Answers true if this object is either equivalent to, or can be 'improved'
+   * by, the given entry. Specifically, answers true if
+   * <ul>
+   * <li>source and accession are identical</li>
+   * <li>version is identical, or this version is of the format "someSource:0",
+   * in which case the version for the other entry replaces it</li>
+   * <li>mappings are not compared but if this entry has no mapping, replace
+   * with that for the other entry</li>
+   * </ul>
+   * 
+   * @param otherEntry
+   * @return
+   */
+  public boolean updateFrom(DBRefEntryI otherEntry);
+
+  /**
+   * Method to distinguish between direct and indirect database references
+   * 
+   * primary references indicate the local sequence data directly corresponds
+   * with the database record. All other references are secondary. direct
+   * references indicate that part or all of the local sequence data can be
+   * mapped with another sequence, enabling annotation transfer.
+   * cross-references indicate the local sequence data can be corresponded to
+   * some other linear coordinate system via a transformation.
+   * 
+   * This method is also sufficient to distinguish direct DBRefEntry mappings
+   * from other relationships - e.g. coding relationships (imply a 1:3/3:1
+   * mapping), but not transcript relationships, which imply a (possibly
+   * non-contiguous) 1:1 mapping
+   * 
+   * The only way a dbref's mappings can be fully verified is via the local
+   * sequence frame, so rather than use isPrimary directly, please use
+   * SequenceI.getPrimaryDbRefs()
+   *
+   * @return true if this reference provides a primary accession for the
+   *         associated sequence object
+   */
+  public boolean isPrimary();
 }